OME_HOST = os.getenv('OME_HOST', 'localhost')
OME_USER = os.getenv('OME_USER', 'test')
OME_PASSWD = os.getenv('OME_PASSWD', 'test')
kb = KB(driver='omero')(OME_HOST, OME_USER, OME_PASSWD)
fn = sys.argv[1] # "affy_na32_reannot_vids.tsv"
outfn = sys.argv[2] # "affy_na32_markers_set_def.tsv"
with open(fn) as f:
reader = csv.DictReader(f, delimiter="\t")
records = [r for r in reader]
vids = [r['source'] for r in records]
markers = kb.get_snp_markers(vids=vids, col_names=['vid', 'mask'])
with open(outfn, 'w') as outf:
fieldnames = ['marker_vid', 'marker_indx', 'allele_flip']
writer = csv.DictWriter(outf,
delimiter="\t",
lineterminator=os.linesep,
fieldnames=fieldnames)
writer.writeheader()
for i, (m, r) in enumerate(it.izip(markers, records)):
assert m.id == r['source']
try:
_, stored_alleles, _ = snp.split_mask(m.mask)
except ValueError:
sys.stdout.write("WARNING: could not split mask for %r\n" %
r['source'])
OME_HOST = os.getenv('OME_HOST', 'localhost')
OME_USER = os.getenv('OME_USER', 'test')
OME_PASSWD = os.getenv('OME_PASSWD', 'test')
kb = KB(driver='omero')(OME_HOST, OME_USER, OME_PASSWD)
fn = sys.argv[1] # "affy_na32_reannot_vids.tsv"
outfn = sys.argv[2] # "affy_na32_markers_set_def.tsv"
with open(fn) as f:
reader = csv.DictReader(f, delimiter="\t")
records = [r for r in reader]
vids = [r['source'] for r in records]
markers = kb.get_snp_markers(vids=vids, col_names=['vid', 'mask'])
with open(outfn, 'w') as outf:
fieldnames = ['marker_vid', 'marker_indx', 'allele_flip']
writer = csv.DictWriter(outf, delimiter="\t", lineterminator=os.linesep,
fieldnames=fieldnames)
writer.writeheader()
for i, (m, r) in enumerate(it.izip(markers, records)):
assert m.id == r['source']
try:
_, stored_alleles, _ = snp.split_mask(m.mask)
except ValueError:
sys.stdout.write("WARNING: could not split mask for %r\n" % r['source'])
flip = False
else:
alleles = r['allele_a'], r['allele_b']
